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The identification of SNPs with indeterminate positions using the Equine SNP50 BeadChip

Corbin, Laura J., Blott, S. C., Swinburne, J. E., Vaudin, M., Bishop, S. C. and Woolliams, J. A. 2012. The identification of SNPs with indeterminate positions using the Equine SNP50 BeadChip. Animal Genetics 43 (3) , pp. 337-339. 10.1111/j.1365-2052.2011.02243.x

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We have used linkage disequilibrium (LD) to identify single nucleotide polymorphisms (SNPs) on the Illumina Equine SNP50 BeadChip, which may be incorrectly positioned on the genome map. A total of 1201 Thoroughbred horses were genotyped using the Illumina Equine SNP50 BeadChip. LD was evaluated in a pairwise fashion between all autosomal SNPs, both within and across chromosomes. Filters were then applied to the data, firstly to identify SNPs that may have been mapped to the wrong chromosome and secondly to identify SNPs that may have been incorrectly positioned within chromosomes. We identified a single SNP on ECA28, which showed low LD with neighbouring SNPs but considerable LD with a group of SNPs on ECA10. Furthermore, a cluster of SNPs on ECA5 showed unusually low LD with surrounding SNPs. A total of 39 SNPs met the criteria for unusual within-chromosome LD. The results of this study indicate that some SNPs may be misplaced. This finding is significant, as misplaced SNPs may lead to difficulties in the application of genomic methods, such as homozygosity mapping, for which SNP order is important.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Business (Including Economics)
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Uncontrolled Keywords: genome; horse; linkage disequilibrium; map; misplacement; order; single nucleotide polymorphism
Publisher: Wiley-Blackwell
ISSN: 0268-9146
Last Modified: 19 Mar 2016 23:22

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